DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
This application 18/050,071 filed on 10/27/2022 is a continuation of U.S. Application No. 16/483,383, filed on 08/02/2019, which is a 371 national phase of PCT/US2018/018859, filed on 02/20/2018, which claims the benefit of provisional U.S. Patent Application No. 62/465,320, filed on 03/01/2017.
The priority date of claim 21 and its dependent claims 22-32 is determined to be 03/01/2017, the filing date of provisional U.S. Patent Application No. 62/465,320.
Status of Claims
Applicant’s amendments to claims filed 01/09/2026 in response to the Non-Final Rejection mailed 08/12/2025 are acknowledged.
Claims 21, 23- 24, 28-31, and 33 are amended.
Claims 21-33 are pending and under examination.
Response to Remarks filed 01/09/2026
The amendments and arguments presented in the papers filed 01/09/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 08/12/2025 listed below have been reconsidered as indicated.
a) The objections to the specification regarding the use of trade names or marks are withdrawn in view of the amendments to the specification.
b) The objections to claim 31 for informalities are withdrawn in view of the amendments to the claim.
c) The 35 USC 112(b) indefiniteness rejections of claims 24 and 30 have been withdrawn in view of the amendments to the claims.
c) The rejection of claims 21-33 Landegren et al. (US PGPub 20140170654, on IDS dated 10/27/2022) in view of Ismagilov et al. (US Pat 11,168,347) are withdrawn in view of amendments to the claims.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Claim Rejections - 35 USC § 112(a) – Scope of Enablement - New
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 21-33 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for adding an exonuclease to the reaction mix in step (c) of claim 21 filed on 01/09/2026, does not reasonably provide enablement for adding any nuclease to the reaction mix in step (c) of claim 21 filed on 01/09/2026. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Nature of the invention/ breadth of the claims/ level of skill in the art.
The claims are drawn to a method for sample analysis. The claims broadly encompass the analysis of a sample using conjugates comprising binding agents and splint oligonucleotides. The claims also broadly encompass any nuclease added to a reaction mix comprising covalently closed circular molecules. The claim further encompass quantifying the amount of covalently closed circular molecules.
The level of one of ordinary skill in the art of this invention is high.
State and predictability of the art.
NEBNucleases (“Nucleases Information”. Retrieved from Wayback Machine on 05/07/2026.https://web.archive.org/web/20150906030448/https://www.neb.com/products/dna-modifying-enzymes-and-cloning-technologies/nucleases/nucleases. Published 09/06/20015) teaches that a “nuclease” includes both endonucleases and exonucleases which act on nucleic acids by different mechanisms. NEBProperties (“Properties of Exonucleases and Endonucleases”. Retrieved from the Wayback Machine on 05/07/2026. https://web.archive.org/web/20150906025907/https://www.neb.com/tools-and-resources/selection-charts/properties-of-exonucleases-and-endonucleases. Published 09/06/2015) further teaches that individual exonucleases and endonucleases are active on different nucleic acid substrates, and further that the amount of enzyme, substrate and time of incubation can have a dramatic effect upon the desired outcome of the experiment.
Thus, there is no evidence to suggest that adding any nuclease to the reaction mix would produce a result that would allow the quantification of the amount of covalently closed circular molecules in the reaction mix. If any nuclease is chosen the covalently closed circular molecules may be degraded and not quantifiable.
Working examples and guidance in the specification.
The claims broadly encompass adding any nuclease to the reaction mix. The specification only provides working examples and guidance for the addition of exonucleases to terminate the ligation and degrade any nucleic acid that is not a covalently closed circular molecule (p. 3, 5, 16, 17, 18, 20, 28, 35 and p. 39, 44 examples). The instant specification further lists specific examples of specific exonucleases that can be used in the method (p. 20).
Amount of experimentation necessary.
Given the variation in nuclease activity and mechanism, the quantity of experimentation necessary to enable the full scope, i.e., the addition of any nuclease to the reaction mix, of the claims is undue.
In view of the teachings above and the lack of guidance, workable examples and
or exemplification in the specification, it would require undue experimentation by one of
skill in the art to determine with any predictability, that the method would function as
claimed.
As such, claims 21-33 contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claim Rejections - 35 USC § 103 - New
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 21-33 are rejected under 35 U.S.C. 103 as being unpatentable over Landegren et al. (US 20140170654, on IDS dated 10/27/2022) in view of Hardenbol et al. (Multiplexed genotyping with sequence-tagged molecular inversion probes. 2003. Nat Biotechnol 21, 673–678) and Ismagilov et al. (US 11,168,347, application 15/715,086 filed on 09/25/2017, claim benefits of US provisional application 62/460,625 filed on 02/17/2017 and US provisional application 62/399193 filed on 09/23/2016).
The following are new rejections necessitated by amendments
Regarding claim 21, Landegren teaches proximity-probe based detection assays for detecting an analyte (target analyte) in a sample.
Regarding step (a), Landegren teaches the method comprises contacting a sample with first and second proximity probes (first and second conjugates) that can simultaneously bind to the analyte, each proximity probe comprising an analyte-binding domain (binding agent) and a nucleic acid domain (splint oligonucleotide) (para 42). Landegren further teaches an analyte-binding domain comprises a protein or fragment thereof (para 103 and 139) (i.e. split into portions).
Regarding step (b), Landegren teaches the nucleic acid domains of the proximity probes when in proximity may template the ligation of one or more added oligonucleotides (i.e., a set of probes) to each other, including an intramolecular ligation to circularize an added linear oligonucleotide (para 7) by the addition of an appropriate ligase (para 92).
Regarding step (d), Landegren teaches quantifying by counting individual reaction products (para 162).
Landegren does not teach step (c), adding a nuclease to the reaction mix.
Hardenbol teaches a method of selecting circularized probes using exonucleases (p. 673, col. 2 – p. 674, col. 1). Hardenbol teaches the addition of exonucleases after ligation forms a circular molecule (Fig. 2). Hardenbol states that the exonuclease reduces the number of linear molecules (p. 674, col. 2 and Fig. 2).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Landegren and Hardenbol arrive at the instantly claimed invention. The modification would have entailed adding the exonuclease of Hardenbol after the addition of ligase to form a circular molecule. Landegren teaches washing wells after adding ligase (para 311), effectively terminating the ligation reaction. One would have been motivated to add exonuclease as in Hardenbol because doing so would degrade linear probes, thus terminating the ligation reaction, and provide the added benefit of enriching the reaction for circular molecules that cannot be digested by the exonuclease. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Landegren is silent on the concentration of target analyte and does not teach a target analyte that is at a concentration of less than 100 nM.
However, Landegren states that the sensitivity of the conventional proximity assays, e.g. proximity ligation assays, is limited by two main factors: (i) the affinity of the analyte-binding domains for the target analyte and (ii) the non-specific background signal arising from the random proximity of non-bound probes.
Moreover, regarding the limitation “target analyte that is at a concentration of less than 100 nM”, Ismagilov et al. teaches digital quantitation of DNA replication and/or chromosome segregation (See Title and abstract) and that “The threshold concentration of target analytes to allow positive signal generation can be at most about 1 fM, 10 fM, 100 fM, 1 pM, 10 pM, 100 pM, 1 nM, 10 nM, 100 nM, 1 μM, 10 μM, 100 μM, 1 mM, 10 mM, 100 mM, 1 M, or less. The threshold number or concentration of target analytes to allow positive signal generation from a reaction volume can be controlled.” (lines 32-36, column 33).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Landegren and Hardenbol to include a target analyte at a concentration of less than 100 nM by incorporating the teachings of Ismagilov. Landegren teaches multiple methods known in the art for controlling sensitivity of the assay (para 16-18) and Ismagilov teaches target analytes at concentrations of less than 100nm (col 33, lines 32-36). It would have been obvious to one with ordinary skill in the art to adjust concentrations of probes or other parameters to arrive at conditions that would enable the methods of Landegren to detect analytes in a sample at a concentration of less than 100nM as taught by Ismagilov. Such optimization would have been routine and ordinary in the art. One would have been motivated to do so for the advantage of optimizing sensitivity of target analyte analysis. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 22, Landegren teaches the analyte binding domain may be a ligand that has even low affinity for its target analyte (para 102)
Regarding claim 23, Landegren teaches quantitatively detecting, for example by realtime quantitative PCR (q-PCR) (para 6).
Regarding claim 24, Landegren does not teach primers used for quantitative PCR target the ligation junctions in the covalently closed circular molecules of (d).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the primers of Landegren to target the ligation junctions in the covalently closed circular molecules. Landegren teaches multiple embodiments of primers (para 210). It would have been obvious to one with ordinary skill in the art to design primers to different regions of the product. The design of primers is routine and ordinary in the art. One would have been motivated to do so for the advantage of optimizing sensitivity of target analyte analysis. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 25, Landegren teaches using rolling circle amplification to amplify the circular nucleic acid molecule template (para 40).
Regarding claim 26, Landegren teaches detection can be performed and quantified by counting individual reaction products (para 162 and see RCA counts in Fig. 17D).
Regarding claim 27, Landegren teaches incubating cells in wells on slides (a vessel), contacting the wells with first and second proximity probes (first and second conjugates), probes and ligase and washing the wells (i.e. terminating the ligation step) (para 311). Thus satisfying the requirement of steps (a)-(c) in the same vessel.
Regarding claim 28, Landegren teaches adding probes and ligases to the slide wells that comprise the product of step (a) and adding TBST+T (reagent) to the wells comprising the ligation product of step (b).
Regarding claim 29, Landegren teaches contacting a sample with two or more different target analytes with a set of proximity probes for each target analyte (para 189). Landegren further teaches comparison of detected levels or amounts between two or more different target analytes (para 144)
Regarding claim 30, Landegren does not teach at least one of the members of the set of probes of step (b)(i) has a molecular index.
However, Landegren teaches a unique “marker” or identification sequence (e.g. a bar-code sequence) to allow the separate detection and/or quantification of each analyte in the sample (para 140). Landegren teaches the barcode in gap oligonucleotides (para 140). Landegren further teaches using sequencing to quantify “detectable tags” (para 162).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Landegren by incorporating the identification sequence (molecular index) in the probes of step (b). The incorporation of unique sequences into different oligonucleotides (here the probes instead of the gap nucleotide) is routine and ordinary in the art. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 31, Landegren teaches the analyte-binding domain (binding agent) may be a protein (para 151).
Landegren does not specifically teach the target analyte can be an antibody.
However, Landegren teaches an analyte can be any substance e.g. molecule that it is desired to detect by the method of the invention. Further, the analyte can be any substance or entity for which a specific binding partner (e.g. an affinity binding partner) can be developed (para 145).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Landegren for an antibody as the target analyte. Antibodies were known in the art to bind specifically to proteins. The modification would have entailed using a protein to which the antibody binds as the binding agent and incubating with a sample that contains the antibody that binds to the protein. One would have been motivated to make the modification in order to quantify antibody binding to a selected protein. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 32, Landegren teaches the target analyte can be a protein (para 145) and the analyte-binding domain (binding agent) can be a polyclonal antibody (para 151). Landegren further teaches the use of affinity-purified polyclonal antibodies (Table 3).
Regarding claim 33, Landegren teaches the sample is saliva (para 147).
Response to Arguments against Claim Rejection - 35 U.S. C § 103
The response asserts the cited references, alone or in combination, do not teach or suggest a step of "adding a nuclease to the reaction mix" as recited by claim 1 to terminate a ligase reaction (p. 7).
Applicant's arguments, see p.7, filed 01/09/2026, with respect to the
rejection(s) of claim(s) 21-33 under 35 U.S.C. 103 have been fully considered
and are persuasive. Therefore, the rejection has been withdrawn. However, upon
further consideration, a new ground(s) of rejection is made over Landegren et al. (US 20140170654, on IDS dated 10/27/2022) in view of Hardenbol et al. (Multiplexed genotyping with sequence-tagged molecular inversion probes. 2003. Nat Biotechnol 21, 673–678) and Ismagilov et al. (US 11,168,347, application 15/715,086 filed on 09/25/2017, claim benefits of US provisional application 62/460,625 filed on 02/17/2017 and US provisional application 62/399193 filed on 09/23/2016) and is presented above.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
(I). (i). Claims 21-30 and 33 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 11,530,438.
Although the claims at issue are not identical, they are not patentably distinct from each other because application claims 21-30 and 33 are anticipated by the issued patent 11,530,438.
Note: The present application is a CON of US patent No. 11,530,438 B2. There is no prohibition against double patenting since the 35 U.S.C. 121 'shield' refers specifically and only to divisional applications, not continuations (MPEP § 804.01).
Regarding instant claim 1, claim 1 of the ‘438 patent requires incubating a sample of blood plasma or serum comprising a target analyte that is at a concentration of less than 100 nM with: (i) a first conjugate comprising a binding agent and a first splint oligonucleotide, and (ii) a second conjugate comprising a binding agent and a second splint oligonucleotide, wherein the first and second conjugates are a polyclonal antibody that has been affinity purified, split into a first portion and a second portion, and then conjugated to the first and second splint oligonucleotides, under conditions suitable for binding of the binding agents of the first and second conjugates to the target analyte, to produce a product; (b) incubating at least some of the product of step (a) with: (i) a set of probes that produces a ligatable circle only when the probes are hybridized to the first and second splint oligonucleotides; and (ii) a ligase; to produce a reaction mix comprising covalently closed circular molecules; (c) treating at least some of the reaction mix of step (b) with an exonuclease to terminate the ligation and degrade any nucleic acid that is not a covalently closed circular molecule; and
(d) after step (c), quantifying the amount of covalently closed circular molecules produced in step (b). Claim 21 of the ‘438 patent is encompassed by claim 1 of the instant application.
Regarding instant claim 22, claim 2 of the ‘438 patent requires the first and second conjugates bind to the target analyte with a low affinity.
Regarding instant claim 23, claim 3 of the ‘438 patent requires the quantifying step (d) is done by quantitative PCR, digital PCR, by hybridization to a microarray or by sequencing.
Regarding instant claim 24, claim 4 of the ‘438 patent requires wherein the primers used for the quantitative PCR target the ligation junctions in the covalently closed circular molecules of (d).
Regarding instant claim 25, claim 5 of the ‘438 patent requires step (d) comprises amplifying the covalently closed circular molecules by rolling circle amplification (RCA) to produce RCA products.
Regarding instant claim 26, claim 6 of the ‘438 patent requires the method comprises counting the RCA products.
Regarding instant claim 27, claim 7 of the ‘438 patent requires the reactions of steps (a)-(c) are done in the same vessel.
Regarding instant claim 28, claim 8 of the ‘438 patent requires step (b) comprises adding the set of probes and ligase to the vessel comprising the product of step (a), and step (c) comprises adding one or more exonucleases to the vessel comprising the ligation product of step (b).
Regarding instant claim 29, claim 9 of the ‘438 patent requires (i) the sample comprises a plurality of target analytes, (ii) step (a) comprises incubating the sample with multiple pairs of said first and second conjugates, wherein each pair of conjugates binds to a different target analyte; and (iii) step (d) comprises quantifying the number of covalently closed circular molecules corresponding to each target analyte.
Regarding instant claim 30, claim 11 of the ‘438 patent requires at least two members of the set of probes of step (b)(i) each have a molecular index; and step (d) is done by i. sequencing the covalently closed circular molecules and then ii counting the number of covalently closed circular molecules using the index sequence, which satisfies the requirement of claim 30: “at least one of the members of the set of probes of step (b)(i) each have a molecular index”.
Regarding instant claim 33, claim 1 of the ‘438 patent requires a sample of blood plasma or serum.
(ii). Claims 31 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 11,530,438 in view of Landegren et al. (US 20140170654, on IDS dated 10/27/2022).
Regarding instant claims 31 and 32, the claims of the ‘438 patent do not require: the target analyte is antibody, and the binding agent is protein to which the antibody binds (instant claim 31); or the binding agent is an affinity purified polyclonal antibody (instant claim 32)
The teachings of Landegren as they relate to these claims are given previously in this office action and are fully incorporated here.
Response to Arguments against Double Patenting
The response requests that the double patenting rejection be held in abeyance until such time as claims in this Application be deemed allowable.
Applicant's arguments have been fully considered but are not persuasive.
No terminal disclaimer has been filed and no argument has been presented against the double patenting rejections. Thus, for the reasons stated above, and those already of the record, the rejection is maintained.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA GRAY whose telephone number is (571)272-0116. The examiner can normally be reached Monday-Friday 8-5 with second Fridays off.
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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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